Although complex diseases represent a critical challenge for human genetics, birth defects represent one class of complex diseases that remain largely unresolved. Because of phenotypic and genetic heterogeneity, the role of environmental factors, and the rarity of extended pedigrees and well-stratified cohorts, birth defects are difficult to study by conventional genetic methods. Nonetheless, the societal burden imposed by birth defects is enormous. This application will take advantage of an efficient, established birth defect gene discovery pipeline that focuses on important birth defects associated with balanced chromosomal rearrangements. In these cases, we will identify genes that are disrupted by the rearrangement breakpoints, and we will test the hypothesis that the genes disrupted by breakpoints are causal for the subject's phenotype. To test the validity of the candidate genes identified, two further strategies will be employed: (1) mutational analysis of phenotypically similar cases that do not involve chromosomal rearrangements, to search for intragenic mutations in the candidate gene, and (2) recapitulation of key aspects of the proband's phenotype in the mouse by targeted mutation or knockdown of the candidate gene. The endpoint for these analyses is to obtain conclusive evidence that the gene disrupted by chromosomal rearrangement in any given case is responsible for the associated birth defects, and to conduct an initial analysis of the gene's developmental function. To accomplish these goals, we will employ a robust accrual system to recruit cases of interest from both national outreach and from major commercial cytogenetic providers. To take maximal advantage of the expertise that already exists within our laboratory, we will restrict our scope to two cases per year (ten overall) and we will focus specifically upon cases that affect organogenesis of the eye, kidney and craniofacial complex. In Aim 1, we will ascertain cases involving balanced chromosomal rearrangements (i.e., translocations and inversions) that are associated with disorders of craniofacial, ocular or renal development, and we will map the rearrangement breakpoints. In Aim 2, we will identify candidate genes disrupted by the breakpoints and determine the relevant mutational mechanisms. In Aim 3, to establish causality for these candidate genes, we will perform mutational analyses of phenotypically related human cases, and in Aim 4 we will further seek to establish causality by using genetic means to recapitulate the phenotype in mouse, and we will also determine the gene's developmental function. This powerful gene discovery approach will identify human genes that are newly linked to medically important birth defects, and help to define their developmental functions. PUBLIC HEALTH REVELANCE: This grant proposes to identify genes that are broken by naturally occurring human chromosome abnormalities associated with congenital birth defects. We will focus on birth defects involving the craniofacial region (e.g., cleft lip and palate), the eye (e.g., congenital cataracts), and the kidney (e.g., vesicoureteral reflux, or VUR). To prove that the broken genes are causally linked to the accompanying birth defect, we will search for mutations in the same gene in other patients with the same birth defect, and we will investigate the consequences of mutating the gene in mice.